Alfalfa variety r413a316

ABSTRACT

The invention relates to the alfalfa variety designated R413A316. Provided by the invention are the seeds, plants and derivatives of the alfalfa variety R413A316. Also provided by the invention are tissue cultures of the alfalfa variety R413A316 and the plants regenerated therefrom. Still further provided by the invention are methods for producing alfalfa plants by crossing the alfalfa variety R413A316 with itself or another alfalfa variety and plants produced by such methods.

BACKGROUND OF THE INVENTION Field of the Invention

The present invention relates generally to the field of alfalfabreeding. In particular, the invention relates to the novel alfalfavariety R413A316.

Description of Related Art

There are numerous steps in the development of any novel plantgermplasm. Plant breeding begins with the analysis and definition ofproblems and weaknesses of the current germplasm, the establishment ofprogram goals, and the definition of specific breeding objectives. Thenext step is selection of germplasm that exhibit the traits to meet theprogram goals. The goal is to combine in a single variety an improvedcombination of traits from the parental germplasm. These selectiontraits may include higher forage yield; increased seed yield; improvedfeed quality, including improved digestability and improved milkconversion by ruminant animals; resistance to diseases and insects;augmented stems and roots; increased abiotic stress tolerance; increaseddrought and heat tolerance; strong stand establishment; improvedagronomic quality and standability traits; resistance to herbicides;winter hardiness; and improvements in compositional traits to meetcurrent and future agronomic practices.

Alfalfa (Medicago sativa L.), also known as lucerne, is a valuableforage legume. Thus, a goal of plant breeders is to develop stable,high-yielding alfalfa varieties that are agronomically sound. Thereasons for this goal include, but are not limited to, maximizing theamount of commodity plant product, e.g., hay, pasture, and silage,produced on the land used; supplying food for humans and animals; andreplenishing nutrients depleted from the soil. To accomplish this goal,the breeder must select and develop alfalfa plants that have the traitsthat result in agronomically superior varieties.

Alfalfa is grown worldwide as forage for livestock, especially cattle.Alfalfa is among the highest-yielding forage crop species, but it is thecombination of high yield and nutritional quality that make alfalfa sucha valuable crop. Alfalfa is most often harvested as hay, but is alsograzed, made into silage, and fed as greenchop. Alfalfa is primarilyused to feed high-producing dairy cows, but is also a food source forbeef cattle, horses, sheep, goats, rabbits, and poultry. Humans consumealfalfa sprouts and incorporate dehydrated alfalfa into dietarysupplements.

Alfalfa, like other legumes, have root nodules that containSinorhizobium meliloti, bacteria that are effective at fixing nitrogen.Alfalfa therefore is also utilized to replenish nitrogen following cropswithout the ability to fix nitrogen in crop rotation.

The commercial production of seeds for growing alfalfa varietiesnormally involves three stages, the production of breeder, foundation,and then certified seed. Breeder seed is the initial seed produced by anintercross of selected parental plants, and thus represents the initialgeneration of an experimental cultivar. A portion of the breeder seed isthen used for small plot forage trials and characterization of thealfalfa variety. Another portion of the breeder seed can be grown inisolation from other alfalfa plants to produce the foundation seed.Foundation seed is then grown in isolation from other alfalfa plants toproduce the certified seed. The certified seed is typically what is soldfor commercial crop production. Allele frequencies across breeder,foundation, and certified seed are maintained.

SUMMARY OF THE INVENTION

One aspect of the present invention relates to seed of alfalfa varietyR413A316. Another aspect of invention relates to plants produced bygrowing a seed of alfalfa variety R413A316 and any plant part thereof. Aplant part as recited herein may be, but is not limited to, leaves,roots, root tips, root hairs, anthers, pistils, stamens, pollen, ovules,flowers, seeds, embryos, stems, buds, cotyledons, hypocotyls, cells andprotoplasts. The invention further provides a tissue culture ofregenerable cells or protoplasts and the alfalfa plants that may beregenerated from such a tissue culture. The regenerable cells andprotoplasts of the invention may be derived from a plant of alfalfavariety R413A316 or plant part thereof, and the plants regeneratedtherefrom are capable of expressing all the morphological andphysiological characteristics of a plant grown from a seed of alfalfavariety R413A316.

In a further aspect, the invention provides a composition comprising aseed of alfalfa variety R413A316 that is comprised in plant seed growthmedia. In certain embodiments, the plant seed growth media is a soil orsynthetic cultivation medium. In specific embodiments, the growth mediamay be comprised in a container or may, for example, be soil in a field.Plant seed growth media are well known to those of skill in the art andinclude, but are in no way limited to, soil or synthetic cultivationmedium. Plant seed growth media can provide adequate physical supportfor seeds and can retain moisture and/or nutritional components.Examples of characteristics for soils that may be desirable in certainembodiments can be found, for instance, in U.S. Pat. Nos. 3,932,166 and4,707,176. Synthetic plant cultivation media are also well known in theart and may, in certain embodiments, comprise polymers or hydrogels, andexamples of such compositions are described, for example, in U.S. Pat.No. 4,241,537.

A further aspect of the invention is a method for producing a firstgeneration of progeny alfalfa seed. The method comprises crossing aplant of alfalfa variety R413A316 with itself or a second alfalfa plantand harvesting the resultant alfalfa seed. In particular embodiments,the second alfalfa plant may be another plant of alfalfa varietyR413A316. The invention further provides for the first generationalfalfa seed produced by this method and the plants grown from thoseseeds.

Another embodiment of the invention is a method of vegetativelypropagating a plant of alfalfa variety R413A316. The method comprisingthe steps of: (a) collecting a tissue capable of being propagated from aplant of alfalfa variety R413A316; (b) cultivating that tissue to obtainproliferated shoots; and (c) rooting those proliferated shoots to obtainrooted plantlets. In particular embodiments, this method furthercomprises the following step: (d) growing a plant from the rootedplantlets.

The invention further provides for a method of modifying a plant ofalfalfa variety R413A316. The method comprises introducing a transgeneor a single locus conversion into a plant of alfalfa variety R413A316.The invention also provides for the alfalfa plants produced by thismethod. In specific embodiments, the plants produced by this methodcomprise a transgene or single locus that comprises a nucleic acidsequence that enables site-specific genetic recombination or confers atrait selected from the group consisting of male sterility, herbicidetolerance, insect resistance, pest resistance, disease resistance,improved digestibility, improved energy content, improved forage or seedyield, improved winterhardiness, improved nitrogen fixation, modifiedfatty acid metabolism, abiotic stress resistance, flowering time,altered seed amino acid composition, and modified carbohydratemetabolism. The seeds that produce the plants generated by this methodare also contemplated by the invention.

Still yet another embodiment of the invention is a method to introduce asingle-locus conversion into a plant of alfalfa variety R413A316. Themethod comprises the following steps: (a) crossing a plant of alfalfavariety R413A316 with a second alfalfa plant to produce a firstgeneration of progeny plants, wherein the second alfalfa plant comprisesthe single locus; and (b) selecting a progeny plant that comprises thesingle locus. In specific embodiments, the single locus introduced intoa plant of alfalfa variety R413A316 comprises a transgene. Still yetanother embodiment of this invention is a method for introducing atransgene or a single locus conversion into a population of alfalfaplants. This method comprises the following steps: (a) modifying a plantof alfalfa variety R413A316 by introducing a transgene or a single locusconversion; and (b) crossing that modified alfalfa plant with apopulation of alfalfa plants to produce a population of progeny plants,wherein at least a progeny plant comprises the transgene or single locusconversion. In particular embodiments, this method further comprises thefollowing step: (c) applying selection techniques to the populationproduced in step (b) to select the progeny plants that comprise thetransgene or single locus conversion. The invention further provides forthe alfalfa plants produced by this and the foregoing method as well asthe seeds that can produce these plants.

Another embodiment provided by this invention is a method of producing asynthetic alfalfa variety. The method comprises combining the seed ofalfalfa variety R413A316 with the seed of a second alfalfa variety. Yetanother embodiment is a method of producing a commodity plant product.This method comprises producing the commodity plant product from a plantof alfalfa variety R413A316. In specific embodiments the commodity plantproduct is selected from a group consisting of sprouts, forage, hay,greenchop, and silage. The invention further provides for the commodityplant product produced by this method, wherein the commodity plantproduct comprises at least one cell of alfalfa variety R413A316.

DETAILED DESCRIPTION OF THE INVENTION

The instant invention provides methods and composition relating toplants, seeds, and derivatives of alfalfa variety R413A316. Alfalfavariety R413A316 is adapted to the North Central, East Central,Winterhardy Intermountain and Moderately Winterhardy Intermountainregions and is very winterhardy. Alfalfa variety R413A316 has beentested in Washington, Idaho, Iowa, Wisconsin and Pennsylvania. Alfalfavariety R413A316 is suitable for use in producing hay, haylage,greenchop or dehydration.

Alfalfa variety R413A316 is a synthetic variety with 110 parent plants.Parent plants contained the commercial Roundup Ready event J-101 andwere selected from breeding populations previously selected forglyphosate tolerance, forage yield, forage quality, persistence and/orresistance to one or more of the following pests: potato leafhopper,bacterial wilt, Fusarium wilt, Verticillium wilt, anthracnose,Phytophthora root rot, stem nematode, northern root knot nematode, andAphanomyces root rot (Race 1 and Race 2). Phenotypic selection was usedto identify the parent plants. The following germplasm sources were usedin the development of this variety: various FGI experimental populations(100%). Syn1 seed was harvested in total on all parents and bulked toform breeder seed in 2013.

Alfalfa variety R413A316 is a Moderately Dormant variety similar tocheck variety FD4. Alfalfa variety R413A316 flower color is 94% purple,3% cream, 2% variegated with a trace of white and yellow.

As disclosed herein above, alfalfa variety R413A316 contains EventJ-101. Event J-101, also known as event MON-00101-8, confers glyphosateherbicide tolerance to alfalfa plants and is the subject of U.S. Pat.Nos. 7,566,817; 8,124,848; and 9,068,196, the disclosures of which areincorporated herein by reference.

The total yield, mean annual yield, persistence, fall dormancy, andwinter survival of alfalfa variety R413A316 were also analyzed andcomparisons were made with selected varieties. The results of theseanalyses are presented in the tables that follow.

Alfalfa variety R413A316 is highly resistant to anthracnose (Race 1),bacterial wilt, Fusarium wilt, Verticillium wilt, Phytophthora root rot,Aphanomyces root rot (Race 1), Aphanomyces root rot (Race 2), and stemnematode; and resistant to pea aphid. All disease and pest tests ofalfalfa variety R413A316 were conducted for the National Alfalfa andMiscellaneous Legume Variety Review Board AOSCA certification and wereconducted by standard procedures and scoring systems as described in theNAAIC Standard Tests to Characterize Alfalfa Cultivars, which aremaintained online on the NAAIC's website. The results of these analysesare presented in the tables that follow.

TABLE 1 Total yield of alfalfa variety R413A316 compared to othervarieties at multiple locations. Mo/Yr Yr No. R413A316 Check 1: Check 2:Check 3: Test Location Planted Harvested Cuts (Syn 1) 54R02 Consistency4.10RR WL 355RR LSD .05 CV % West Salem, WI 8/13 2014 4 7.92 7.18 7.027.48 0.51 4.84 2015 4 8.02 6.37 6.31 6.66 0.64 6.18 2016 4 9.20 6.556.88 6.67 0.76 6.68 Boone, IA 8/13 2014 4 5.89 5.82 5.66 5.04 0.75 9.242015 4 5.95 5.78 5.24 5.25 0.75 9.08 Nampa, ID 8/13 2014 6 11.89 10.919.73 10.89 1.32 8.58 2015 6 11.80 10.77 9.59 10.81 1.17 7.21 2016 5 9.148.41 8.07 8.35 0.77 5.78 Mt Joy, PA 8/13 2014 5 8.39 8.45 8.50 8.02 0.706.09 2015 5 8.72 7.91 7.94 7.91 0.95 8.60 Touchet, WA 8/13 2014 6 12.2612.17 10.99 10.81 0.91 5.44 2015 6 13.22 12.17 11.49 11.12 0.85 4.70

TABLE 2 Mean annual yield of alfalfa variety R413A316. # of Years Total# of R413A316 Check 1: Check 2: Check 3: Variety names HarvestedHarvests (Syn 1) 54R02 Consistency 4.10RR WL 355RR R413A316 (Syn 1) 1259 9.37 Check 1: 54R02 12 59 9.37 8.54 Check 2: Consistency 4.10RR 12 599.37 8.12 Check 3: WL 355RR 12 59 9.37 8.13

TABLE 3 Persistence of alfalfa variety R413A316 compared to othervarieties. Mo/Yr of Mo/Yr No. of Yrs No. of Readings R413A316 54R02 WL355RR Test Location Seeded Harvested Harvests Initial/Final (Syn 1)Initial/Final Initial/Final LSD .05 CV % W Salem, WI 8/13 3 12(9/13)/(9/16) 100/82 100/75 100/75 7.7 9.1

TABLE 4 Fall dormancy of alfalfa variety R413A316 as determined fromspaced plantings relative to three check varieties. Variety FallDormancy Class Unadjusted FDR R413A316 (Syn 1) 4 4.2 5246 3 3.0 D Legend4 3.9 MD Archer 5 4.9 MD Test Mean: 4.3 L.S.D._((0.05%)) 0.42 C.V. (%)3.49 Test conducted in 2013 by Forage Genetics at West Salem, WI. Dateof Last Cut (Mo/Yr): 9/13. Date Measured (Mo/Yr): 10/13. VD (VeryDormant)/D (Dormant)/MD (Moderately Dormant)/ND (Non-Dormant)/VND (VeryNon-Dormant).

TABLE 5 Winter survival rating of alfalfa variety R413A316 compared toother varieties. Mo/Yr Mo/Yr R413A316 ZG 9830 5262 WL325 HQ G-2852Archer CUF 101 Test Location Planted Measured (Syn 1) -1- -2- -3- -4--5- -6- LSD .05 CV % W. Salem, WI 5/13 5/14 2.4 1.5 2.5 2.8 3.3 3.6 5.00.30 9.9 Boone, IA 5/13 5/14 1.9 1.7 1.9 2.9 4.4 4.5 5.0 0.32 9.5 1 =Extremely Winterhardy; 2 = Very Winterhardy; 3 = Winterhardy; 4 =Moderately Winterhardy; 5 = Slightly Winterhardy; and 6 =Non-Winterhardy.

TABLE 6 MULTIFOLIOLATE LEAF EXPRESSION score for alfalfa varietyR413A316. Multifoliolate Leaf Variety Range Expression Score MFI % MFR413A316 (Syn 1) High 3.15 83 Legend 1.40-2.40 Low 1.42 58 MultiKing I2.00-3.00 Moderate 2.64 70 Proof 2.80-3.80 High 3.41 93 Test Mean: 2.7477 L.S.D. (.05%) 0.36 8.0 C.V. (%) 13.3 10.6 Test conducted in 2015 byForage Genetics at Nampa, ID.

TABLE 7 Glyphosate herbicide tolerance rating for alfalfa varietyR413A316. Unadjusted Adjusted Variety Tolerance Class % R % R R413A316(Syn 1) HT 92 91 FGI-RR90 HT 91 90 Saranac NT 0 0 Test Mean: 91 90L.S.D. (.05%) 2 C.V. (%) 1.6 Test conducted in 2016 by Forage Geneticsat West Salem, WI. Kind of test conducted: Lab. HT = herbicide tolerant(≥90% glyphosate tolerant); NT = not herbicide tolerant.

TABLE 8 ANTHRACNOSE DISEASE (Race 1) score for alfalfa variety R413A316.Unadjusted Adjusted Variety Resistance Class % R % R R413A316 (Syn 1) HR75 75 Arc HR 68 68 Saranac S 1 1 Test Mean: 62 62 L.S.D. (.05%) 10 C.V.(%) 11.4 Test conducted in 2013 by Forage Genetics at West Salem, WI.Kind of test conducted: Greenhouse. S = <6%, LR = 6-14%, MR = 15-30%, R= 31-50%, HR = >50%.

TABLE 9 BACTERIAL WILT DISEASE score for alfalfa variety R413A316.Unadjusted Adjusted Variety Resistance Class % R % R R413A316 (Syn 1) HR51 58 Vernal R 37 42 Sonora S 0 0 Test Mean: 58 66 L.S.D. (.05%) 13 C.V.(%) 16.5 Test conducted in 2015 by Forage Genetics at West Salem, WI.Kind of test conducted: Field. S = <6%, LR = 6-14%, MR = 15-30%, R =31-50%, HR = >50%.

TABLE 10 FUSARIUM WILT DISEASE score for alfalfa variety R413A316.Unadjusted Adjusted Variety Resistance Class % R % R R413A316 (Syn 1) HR59 66 Agate GH R 40 45 MNGN-1 S 4 5 Test Mean: 57 64 L.S.D. (.05%) 11C.V. (%) 13.8 Test conducted in 2015 by Forage Genetics at Nampa, ID.Kind of test conducted: Greenhouse. S = <6%, LR = 6-14%, MR = 15-30%, R= 31-50%, HR = >50%.

TABLE 11 VERTICILLIUM WILT DISEASE score for alfalfa variety R413A316.Unadjusted Adjusted Variety Resistance Class % R % R R413A316 (Syn 1) HR65 65 Oneida VR HR 60 60 Saranac S 3 3 Test Mean: 50 50 L.S.D. (.05%) 11C.V. (%) 15.0 Test conducted in 2015 by Forage Genetics at Nampa, ID.Kind of test conducted: Greenhouse. S = <6%, LR = 6-14%, MR = 15-30%, R= 31-50%, HR = >50%.

TABLE 12 PHYTOPHTHORA ROOT ROT DISEASE score for alfalfa varietyR413A316. Unadjusted Adjusted Variety Resistance Class % R % R R413A316(Syn 1) HR 50 55 WAPH-1 (seedling) HR 50 55 Saranac S 0 0 Test Mean: 4853 L.S.D. (.05%) 10 C.V. (%) 13.1 Test conducted in 2014 by ForageGenetics at West Salem, WI. Kind of test conducted: Seedling. S = <6%,LR = 6-14%, MR = 15-30%, R = 31-50%, HR = >50%.

TABLE 13 APHANOMYCES ROOT ROT (RACE1) DISEASE score for alfalfa varietyR413A316. Unadjusted Adjusted Variety Resistance Class % R % R R413A316(Syn 1) HR 58 59 WAPH-1 (Race 1) R 49 50 Saranac (Races 1 & 2) S 0 0Test Mean: 53 54 L.S.D. (.05%) 7 C.V. (%) 8.2 Test conducted in 2014 byForage Genetics at West Salem, WI. Kind of test conducted: Greenhouse. S= <6%, LR = 6-14%, MR = 15-30%, R = 31-50%, HR = >50%.

TABLE 14 PEA APHID INSECT score for alfalfa variety R413A316. UnadjustedAdjusted Variety Resistance Class % R % R R413A316 (Syn 1) R 38 46 PA-1HR 46 55 Vernal S 3 4 Test Mean: 41 49 L.S.D. (.05%) 8 C.V. (%) 12.2Test conducted in 2016 by Forage Genetics at Nampa, ID. Kind of testconducted: Greenhouse. S = <6%, LR = 6-14%, MR = 15-30%, R = 31-50%, HR= >50%.

TABLE 15 SPOTTED ALFALFA APHID INSECT score for alfalfa varietyR413A316. Unadjusted Adjusted Variety Resistance Class % R % R R413A316(Syn 1) HR 46 56 Vernema HR 49 60 Ranger LR 7 8 Test Mean: 33 40 L.S.D.(.05%) 8 C.V. (%) 12.9 Test conducted in 2016 by Forage Genetics atNampa, ID. Kind of test conducted: Greenhouse. S = <6%, LR = 6-14%, MR =15-30%, R = 31-50%, HR = >50%.

TABLE 16 APHANOMYCES ROOT ROT (RACE 2) DISEASE score for alfalfa varietyR413A316. Unadjusted Adjusted Variety Resistance Class % R % R R413A316(Syn 1) HR 49 64 WAPH-5 R 38 50 Saranac S 2 2 WAPH-1 S 2 2 Test Mean: 4255 L.S.D. (.05%) 9 C.V. (%) 13.5 Test conducted in 2014 by ForageGenetics at West Salem, WI. Kind of test conducted: Lab. S = <6%, LR =6-14%, MR = 15-30%, R = 31-50%, HR = >50%.

Breeding Alfalfa Variety R413A316

One aspect of the current invention concerns methods for crossingalfalfa variety R413A316 with itself or a second plant and the seeds andplants produced by such methods. These methods can be used to furtherpropagate alfalfa variety R413A316 by increasing the volume of seedavailable to farmers for the commercial production of commodityproducts. Or, these methods can be used to produce novel alfalfa strainsand varieties. Alfalfa variety R413A316 is well-suited to thedevelopment of new strains and varieties based on the elite nature ofits genetic background.

The goal of plant breeding is to develop new, unique, and agronomicallysuperior varieties. The breeding and selection methods employed to dothis depend on the mode of plant reproduction, the heritability of thetrait(s) being improved, and the type of variety used commercially,e.g., synthetic variety, F₁ hybrid variety, pureline variety, etc.Alfalfa breeding is particularly complex because alfalfa has anautotetraploid genome and is normally self-incompatible, i.e., little orno viable seed is produced when alfalfa is selfed. Producing truebreeding alfalfa parents is therefore not possible by traditionalinbreeding techniques, and alfalfa breeders must be careful to avoidinbreeding depression when cross-breeding very small alfalfapopulations. Inbreeding depression in alfalfa populations can result inreduced yield performance, loss of traits of interest as well as adecline in agronomic performance.

To improve alfalfa germplasm pools or varieties, a breeder willinitially polycross two or more plants, generally using insectpollinators, and grow the resulting seed. These progeny plants areevaluated over multiple years and geographical, climatic, and soilconditions. Based on these field evaluations, a breeder will select theplants from this progeny population to advance to another generation ofintermating and selection. These progeny plants are typicallyintermated, and the resultant seed is grown, often in half-sib rows, andevaluated in field trials. This process of evaluating, selecting,advancing, and intermating may continue iteratively for multiple cycles.Throughout this entire process, a breeder is simultaneously selectingthe individual plants that will be incorporated into a distinct“parental” population which will be intermated to generate the newalfalfa variety. These “parental” plants can be selected at any stage inthe breeding process and a breeder will typically select two to hundredsof “parental” plants to generate a new alfalfa variety.

The individual morphological and physiological characteristics of thealfalfa varieties that are developed by the above process as well astheir cumulative morphological and physiological profiles, which areeach unique composites of these individual characteristics, cannot beentirely or precisely expected or predicted at the outset of such aprocess. This is because all plant selections occur in uniqueenvironments with no control over the chromosomal segregation that isoccurring at the DNA level (using conventional breeding procedures), andtherefore millions of different genetic combinations, if not more, arepossible. At the outset of any alfalfa breeding program, a breeder ofordinary skill in the art cannot expect or predict the final resultingvarieties, except potentially in a gross and general fashion, and thesame breeder would not expect to produce the same variety twice bymerely intermating the exact same original “parental” plants andemploying the same selection techniques. This unpredictability resultsin the expenditure of large amounts of research monies to developagronomically superior new alfalfa varieties.

An advanced experimental population is evaluated with check varieties inenvironments that are representative of the commercial target area(s).The best lines are selected as new commercial varieties. These varietiesmay be used as parents to produce future populations for furtherselection. These processes, which lead to the final step of marketingand distribution, may take as much as 8 to 12 years from the time thefirst cross is made. Development of new alfalfa varieties is atime-consuming process that requires precise breeding skill, forwardplanning, and focused directional changes.

In selecting plants to cross with a plant of alfalfa variety R413A316for the purpose of developing unique future novel alfalfa varieties, oneof skill in the art would typically select those plants that exhibit oneor more agronomically significant characteristics that are distinct fromthose exhibited by alfalfa variety R413A316, such as, but not limitedto, disease, insect, or nematode resistance, herbicide tolerance,persistence, adaptation to specific environments, increased forageyield, and improved forage quality.

The true genotypic value for most traits can be masked by otherconfounding traits or environmental factors. The complexity ofinheritance of any trait may influence the choice of selection method.The evaluation and identification of a superior individual alfalfa plantis based on the observed performance of that variety relative to that ofstandard commercial check varieties and other experimental varieties.Replicated observations, e.g., progeny test, provide a better predictionof genetic worth than single observations for traits with lowheritabiltiy. In contrast, evaluating individual plants at a singlelocation may be sufficient for selecting highly heritable traits.

The development of agronomically superior alfalfa plants may also befacilitated by employing specific breeding strategies. Popular selectionmethods that incorporate breeding strategies commonly include pedigreeselection, modified pedigree selection, mass selection, recurrentselection, and backcrossing. Again, the means by which alfalfareproduces, the expected degree of inbreeding depression, and theheritability of a particular trait may influence the choice of breedingmethod. Backcross breeding is used to transfer one or more genes for ahighly heritable trait into an agronomically superior variety. Forinstance, this approach has been used extensively for breedingdisease-resistant varieties (Bowers et al., Crop Sci., 32(1):67-72,1992; Nickell and Bernard, Crop Sci., 32(3):835, 1992). Whereas, variousrecurrent selection techniques can be used to augment quantitativelyinherited traits that can be controlled by numerous genes.

Recurrent selection is another method used to develop varieties frombreeding populations. Breeding populations combine traits from two ormore varieties or various broad-based sources into breeding pools fromwhich varieties are developed by intermating and the subsequentselection of individuals based on phenotype. Mass or recurrent selectioncan be applied to improve populations of cross-pollinating crops likealfalfa. A genetically heterogeneous population, primarily consisting ofheterozygous individuals, is either identified or created byintercrossing several different parents selected for individualagronomically significant characteristics, outstanding progeny, orexcellent combining ability. The selected plants are then intermated toproduce a new population upon which further cycles of selection areapplied.

Backcross breeding has been used to transfer genetic loci for simplyinherited or highly heritable traits into a variety that is used as therecurrent parent. The initial source of the trait to be transferred iscalled the donor or non-recurrent parent. After the F₁ cross,individuals possessing the phenotype or genotype of the donor parent areselected and then may be repeatedly crossed, i.e., backcrossed, to therecurrent parent or a close relative of the recurrent parent, i.e.,modified backcross. The resulting plants are expected to resemble therecurrent parent and are converted for the genetic locus selected fromthe donor parent.

In half-sibling selection, a plant is randomly pollinated by apopulation of plants, and the half-sib seed produced by that femaleparent plant then are grown in progeny rows. The characteristics ofthose progeny rows are then evaluated to inform female parent selection.

Descriptions of other breeding methods that are commonly used fordifferent traits and crops can be found in one of several referencebooks (e.g., Allard, “Principles of Plant Breeding,” John Wiley & Sons,NY, University of California, Davis, Calif., 50-98, 1960; Simmonds,“Principles of Crop Improvement,” Longman, Inc., NY, 369-399, 1979;Sneep et al., “Plant breeding perspectives,” Wageningen (ed), Centre forAgricultural Publishing and Documentation, 1979; and Poehlman andSleper, “Breeding Field Crops”, 4th Ed., Iowa State University Press,Ames, 1995).

Testing of a novel alfalfa variety should detect any major faults andestablish the level of superiority or improvement over current varietiesas well as characterize the improved phenotypic performance of the newvariety for a defined area of adaptation. Characterization for seedproduction is also evaluated as part of the testing process.

Genetically Identifying Alfalfa Varieties

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through amolecular marker profile. Molecular marker profiling can be used atleast to identify plants of the same variety or a related variety, toidentify plants and plant parts which are genetically superior as aresult of an event comprising a backcross conversion, transgene, orgenetic sterility factor, or to determine or validate a pedigree. Suchmolecular marker profiling can be accomplished by using a variety oftechniques including, but not limited to, restriction fragment lengthpolymorphism (RFLP), amplified fragment length polymorphism (AFLP),sequence-tagged sites (STS), randomly amplified polymorphic DNA (RAPD),arbitrarily primed polymerase chain reaction (AP-PCR), DNA amplificationfingerprinting (DAF), sequence characterized amplified regions (SCARs),variable number tandem repeat (VNTR), short tandem repeat (STR), singlefeature polymorphism (SFP), simple sequence length polymorphism (SSLP),restriction site associated DNA, allozymes, isozyme markers, singlenucleotide polymorphisms (SNPs), or simple sequence repeat (SSR)markers, also known as microsatellites (Gupta et al., 1999; Korzun etal., 2001). Various types of marker platforms, for example, can be usedto identify individual varieties developed from specific parentvarieties, as well as cells, or other plant parts thereof. Specific toalfalfa, see, A Saturated Genetic Linkage Map of Autotetraploid Alfalfa(Medicago sativa L.) Developed Using Genotyping-by-Sequencing Is HighlySyntenous with the Medicago truncatula Genome, G3 (Bethesda). 2014October; 4(10): 1971-1979.; Development of an Alfalfa SNP Array and ItsUse to Evaluate Patterns of Population Structure and LinkageDisequilibrium. PLoS ONE. 9(1): e84329.https://doi.org/10.1371/journal.pone.0084329.; and Construction of animproved linkage map of diploid alfalfa (Medicago sativa). Theor. Appl.Genet. 100(5):641-657 (March 2000), which are incorporated by referencefor this purpose.

In some examples, one or more markers may be used to characterize and/orevaluate an alfalfa variety. Particular markers used for these purposesare not limited to any particular set of markers, but are envisioned toinclude any type of marker and marker profile that provides a means fordistinguishing varieties. One method of comparison may be to use onlyhomozygous loci, i.e., nulliplex or quadriplex loci, for alfalfa varietyR413A316. PCR and next-generation sequencing methodologies to identifyand assay these and other markers are disclosed in, for example, ASaturated Genetic Linkage Map of Autotetraploid Alfalfa (Medicago sativaL.) Developed Using Genotyping-by-Sequencing Is Highly Syntenous withthe Medicago truncatula Genome, G3 (Bethesda). 2014 October; 4(10):1971-1979.; Development of an Alfalfa SNP Array and Its Use to EvaluatePatterns of Population Structure and Linkage Disequilibrium. PLoS ONE.9(1): e84329. https://doi.org/10.1371/journal.pone.0084329.;Construction of an improved linkage map of diploid alfalfa (Medicagosativa), Theor. Appl. Genet. 100(5):641-657 (March 2000); and Isolationof a full-length mitotic cyclin cDNA clone CycIIIMs from Medicagosativa: Chromosomal mapping and expression, Plant Mol. Biol.27(6):1059-1070 (1995). In addition to being used for identification ofalfalfa variety R413A316, as well as plant parts and plant cells ofalfalfa variety R413A316, a genetic profile may be used to identify analfalfa plant produced through the use of alfalfa variety R413A316 or toverify the pedigree of progeny plants or a variety produced through theuse of alfalfa variety R413A316. A genetic marker profile may also beuseful in marker-assisted selection or backcrossing.

In an embodiment, the present invention provides an alfalfa varietycharacterized by the molecular and physiological data obtained from arepresentative sample of said variety deposited with the American TypeCulture Collection (ATCC). Thus, plants, seeds, or parts thereof, havingall of the morphological and physiological characteristics of alfalfavariety R413A316 are provided.

In some examples, a plant, a plant part, or a seed of alfalfa varietyR413A316 may be characterized by producing a molecular profile. Amolecular profile may include, but is not limited to, one or moregenotypic and/or phenotypic profile(s). A genotypic profile may include,but is not limited to, a marker profile, such as a genetic map, alinkage map, a trait maker profile, a SNP profile, an SSR profile, agenome-wide marker profile, a haplotype, or the like. A molecularprofile may also be a nucleic acid sequence profile, and/or a physicalmap. A phenotypic profile may include, but is not limited to, a proteinexpression profile, a metabolic profile, an mRNA expression profile, andthe like.

One means of generating genetic marker profiles is to assay SNPs thatare known in the art. Hundreds of thousands of SNPs are known inalfalfa, see Development of an Alfalfa SNP Array and Its Use to EvaluatePatterns of Population Structure and Linkage Disequilibrium. PLoS ONE.9(1): e84329. https://doi.org/10.1371/journal.pone.0084329. A markersystem based on SNPs can be highly informative in linkage analysisrelative to other marker systems, in that multiple alleles may bepresent. Another advantage is that SNPs can be detected through use ofstrategically designed primers, probes, or other specially designedhybridization molecules, which eliminates the need to performlabor-intensive Southern blots. Further, many SNP detection methods areeasily scalable and therefore can easily integrate into high-throughputanalysis platforms such as microarray and next-generation sequencingtechnologies. High density microarray platforms, for example, arecapable of analyzing hundreds of thousands SNPs on a single microarraychip.

A genotypic profile of alfalfa variety R413A316 can be used to identifya plant or population of plants comprising variety R413A316 as a parent,because such plants will comprise the same allelic profile as alfalfavariety R413A316 at an expected frequency by Mendelian inheritance. Inaddition, plants and plant parts substantially benefiting from the useof alfalfa variety R413A316 in their development, such as alfalfavariety R413A316 comprising a backcross conversion, transgene, orgenetic sterility factor, may be identified by having a molecular markerprofile with a high percent identity to alfalfa variety R413A316.

A genotypic profile of alfalfa variety R413A316 also can be used toidentify essentially derived varieties and other progeny varietiesdeveloped from the use of alfalfa variety R413A316, as well as cells andother plant parts thereof. Plants of the invention include any planthaving at least 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%,or 99.9% of the markers in the genotypic profile, and that retain 90%,91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of themorphological and physiological characteristics of alfalfa varietyR413A316 when grown under the same conditions. Such plants may bedeveloped using markers well known in the art. Progeny plants and plantparts produced using alfalfa variety R413A316 may be identified by anymeans known in the art that is indicative or consistent with thevariety. For example, progeny plants and plant parts produced usingalfalfa variety R413A316 may be identified by having a molecular markerprofile of at least 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%,89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 99.5% geneticcontribution from alfalfa variety R413A316 by percent identity orpercent similarity, or such plants may be identified by statisticalgenetic parameters such as, but not limited to, allele frequency andfixation index (F_(ST)). Such progeny may be further characterized asbeing within a pedigree distance of alfalfa variety R413A316, such aswithin 1, 2, 3, 4, or 5 or less cross-pollinations to an alfalfa plantother than alfalfa variety R413A316, or a plant that has alfalfa varietyR413A316 as a progenitor. Unique molecular profiles may be identifiedwith other next-generation sequencing tools, such as SNP discovery orhaplotype analysis.

Any time the alfalfa variety R413A316 is crossed with a different plantor population, F₁ alfalfa progeny is produced. The F₁ progeny isproduced regardless of characteristics of the parental varieties. Assuch, an F₁ alfalfa plant may be produced by crossing a plant of alfalfavariety R413A316 with any second alfalfa plant. The second alfalfa plantmay be genetically homogeneous (e.g., inbred) or may itself be a hybrid.Therefore, any F₁ alfalfa plant produced by crossing a plant of alfalfavariety R413A316 with a second alfalfa plant is a part of the presentinvention.

Further Embodiments of the Invention

In certain aspects of the invention, plants of alfalfa variety R413A316are modified to include at least a first heritable trait. Such plantsmay, in one embodiment, be developed by a plant breeding techniquecalled backcrossing, wherein essentially all of the morphological andphysiological characteristics of a variety are recovered in addition toa genetic locus, or small number of loci, transferred into the plant viathe backcrossing technique. By essentially all of the morphological andphysiological characteristics, it is meant that the characteristics of aplant are recovered that are otherwise present when compared in the sameenvironment, other than occasional variant traits that might ariseduring backcrossing or direct introgression of a transgene. It isunderstood that a locus introduced by backcrossing may or may not betransgenic in origin, and thus the term backcrossing specificallyincludes backcrossing to introduce loci that were created by genetictransformation.

In a typical backcross protocol, the original variety of interest (therecurrent parent) is crossed to a second variety (the non-recurrent ordonor parent) that carries the specific locus or loci of interest to betransferred. The resulting progeny from this cross are then crossedagain to the recurrent parent or a close relative thereof and theprocess can be repeated until an alfalfa plant is obtained whereinessentially all of the morphological and physiological characteristicsof the recurrent parent are recovered in the converted plant, inaddition to the transferred locus from the donor parent.

The selection of a suitable recurrent parent is an important step for asuccessful backcrossing procedure. The goal of a backcross protocol isto alter or substitute a trait or characteristic in the originalvariety. To accomplish this, a locus of the recurrent parent is modifiedor substituted with the desired locus from the donor parent, whileretaining essentially all of the rest of the genome of the originalparent, and therefore the morphological and physiological constitutionof the original variety. The choice of the donor parent will depend onthe purpose of the backcross. One of the primary purposes is to add acommercially or agronomically significant trait to the plant or variety.The specific backcrossing protocol will depend on the characteristic ortrait being altered to determine an appropriate testing protocol.Although backcrossing methods are simplified when the characteristicbeing transferred is a dominant allele, a recessive allele may also betransferred. If the trait of interest is transferred via a recessiveallele, a test of the progeny may be employed to determine if thedesired characteristic has been successfully transferred.

The traditional backcross technique can be adjusted to include more thanone recurrent parent when breeding plants such as alfalfa, in whichhomozygosity can result in inbreeding depression, agronomic performancedecline, and loss of traits of interest. This type of backcrossing isknown as modified backcrossing and employs at least two differentrecurrent parents to produce a sufficiently heterozygous population withthe agronomically significant characteristics of the recurrent parentsand the trait or traits of interest from the donor parent. Modifiedbackcrossing may also be used to replace the original recurrent parentwith one or more distinct parents to stack different characteristicsfrom each, and therefore providing additional improvement over a singlerecurrent parent.

Backcrossing techniques can be used to improve many traits that may notnormally be selection targets when developing a new alfalfa variety.These traits may or may not be transgenic. Examples of these traitsinclude, but are not limited to, male sterility, herbicide resistance,resistance to bacterial, fungal, or viral disease, insect and pestresistance, restoration of male fertility, enhanced nutritional quality,yield stability, and yield enhancement. These comprise genes generallyinherited through the nucleus.

Direct selection may be applied when the locus acts as a dominant trait.An example of a dominant trait is the herbicide resistance trait. Forthis selection process, progeny plants of the initial cross are sprayedwith the herbicide prior to the backcrossing. The spraying eliminatesany plants which do not have the selected herbicide resistancecharacteristic, and only those plants that have the herbicide resistancegene are advanced. This process is then repeated for all additionalgenerations.

Selection of alfalfa plants for breeding is not necessarily dependent onthe phenotype of a plant and instead can be based on geneticinvestigations. For example, one may utilize a suitable genetic markerthat is closely associated with a trait of interest. One of thesemarkers may therefore be used to identify the presence or absence of atrait in the progeny of a particular cross, and hence may be used toselect progeny for continued breeding. This technique may commonly bereferred to as marker assisted selection. Any other type of geneticmarker or other assay that is able to identify the relative presence orabsence, i.e., dosage, of a trait of interest in a plant may also beuseful for breeding purposes. Procedures for marker-assisted selectionapplicable to the breeding of alfalfa are well known in the art. Suchmethods will be of particular utility in the case of recessive traits,phenotypes that are not consistently expressed in selectionenvironments, or when conventional assays may be more expensive,time-consuming or otherwise disadvantageous. Genetic markers that couldbe used in accordance with the invention include, but are notnecessarily limited to, Single Nucleotide Polymorphisms (SNPs), SimpleSequence Length Polymorphisms (SSLPs), Sequence Characterized AmplifiedRegions (SCARs), and Amplified Fragment Length Polymorphisms (AFLPs).Additionally, methods known in the art that generate genetic profilescapable of distinguishing between different genotypes can be used inaccordance with the invention and include, but are not necessarilylimited to, next-generation sequencing technologies, microarrays,Randomly Amplified Polymorphic DNAs (RAPDs), DNA AmplificationFingerprinting (DAF), and Arbitrary Primed Polymerase Chain Reaction(AP-PCR). Many qualitative characteristics also have a potential use asphenotype-based genetic markers in accordance with this invention.

Many useful traits that can be introduced by backcrossing, as well asdirectly into a plant, are those that are introduced by genetictransformation techniques. Genetic transformation may be used to inserta selected transgene into the alfalfa variety R413A316 or may,alternatively, be used for the preparation of transgenes which can beintroduced by backcrossing. Methods for the transformation of manyeconomically important plants, including alfalfa, are well known tothose of skill in the art. Techniques which may be employed togenetically transform alfalfa include, but are not limited to,electroporation, microprojectile bombardment, Agrobacterium-mediatedtransformation and direct DNA uptake by protoplasts. Specific toalfalfa, see, “Efficient Agrobacterium-mediated transformation ofalfalfa using secondary somatic embryogenic callus,” Journal of theKorean Society of Grassland Science 20 (1):13-18 (2000); E. CharlesBrummer, “Applying Genomics to Alfalfa Breeding Programs” Crop Sci.44:1904-1907 (2004); and “Genetic transformation of commercial breedingpopulations of alfalfa (Medicago sativa)” Plant Cell Tissue and OrganCulture 42(2):129-140 (1995), which are incorporated by reference forthis purpose.

To effect transformation by electroporation, one may employ eitherfriable tissues, such as a suspension culture of cells or embryogeniccallus, or one may transform immature embryos or other organized tissuedirectly. In this technique, one would partially degrade the cell wallsof the chosen cells by exposing them to pectin-degrading enzymes(pectolyases) or mechanically wound tissues in a controlled manner.Protoplasts may also be employed for electroporation transformation ofplants (Bates, Mol. Biotechnol., 2(2):135-145, 1994; Lazzeri, MethodsMol. Biol., 49:95-106, 1995).

Another efficient method for delivering DNA segments to plant cells ismicroprojectile bombardment. In this method, particles are coated withnucleic acids and delivered into cells by a propelling force. Exemplaryparticles include those comprised of tungsten, platinum, or gold. Forthe bombardment, cells in suspension are concentrated on filters orsolid culture medium. Alternatively, immature embryos or other targetcells may be arranged on solid culture medium. The cells to be bombardedare positioned at an appropriate distance below the microprojectilestopping plate.

An illustrative embodiment of a method for delivering DNA into plantcells by acceleration is the Biolistics Particle Delivery System, whichcan be used to propel particles coated with DNA or cells through ascreen, such as a stainless steel or Nytex screen, onto a surfacecovered with target alfalfa cells. The screen disperses the particles sothat they are not delivered to the recipient cells in large aggregates.It is believed that a screen intervening between the projectileapparatus and the cells to be bombarded reduces the size of theprojectile aggregate and may contribute to a higher frequency oftransformation by reducing the damage inflicted on the recipient cellsby projectiles that are too large. Microprojectile bombardmenttechniques are widely applicable, and may be used to transform virtuallyany plant species.

Agrobacterium-mediated transfer is another widely applicable system forintroducing gene loci into plant cells. An advantage of the technique isthat DNA can be introduced into whole plant tissues, thereby bypassingthe need for regeneration of an intact plant from a protoplast. ModernAgrobacterium transformation vectors are capable of replication in E.coli as well as Agrobacterium, allowing for convenient manipulations(Klee et al., Bio. Tech., 3(7):637-642, 1985). Moreover, recenttechnological advances in vectors for Agrobacterium-mediated genetransfer have improved the arrangement of genes and cloning sites in thevectors to facilitate the construction of vectors capable of expressingvarious polypeptide coding genes. Vectors can have convenientmultiple-cloning sites (MCS) flanked by a promoter and a polyadenylationsite for direct expression of inserted polypeptide coding genes. Othervectors can comprise site-specific recombination sequences, enablinginsertion of a desired DNA sequence without the use of restrictionenzymes (Curtis et al., Plant Physiology 133:462-469, 2003).Additionally, Agrobacterium containing both armed and disarmed Ti genescan be used for transformation.

In those plant strains in which Agrobacterium-mediated transformation isefficient, it is the method of choice because of the facile and definednature of the gene locus transfer. The use of Agrobacterium-mediatedplant integrating vectors to introduce DNA into plant cells is wellknown in the art (Fraley et al., Bio. Tech., 3(7):629-635, 1985; U.S.Pat. No. 5,563,055).

Transformation of plant protoplasts also can be achieved using methodsbased on calcium phosphate precipitation, polyethylene glycol treatment,electroporation, and combinations of these treatments. See, e.g.,Potrykus et al., Mol. Gen. Genet., 199(2):169-177, 1985; Omirulleh etal., Plant Mol. Biol., 21(3):415-428, 1993; Fromm et al., Nature,319(6056):791-793, 1986; Uchimiya et al., Mol. Gen. Genet.,204(2):204-207, 1986; Marcotte et al., Nature, 335(6189):454-457, 1988).

Included among various plant transformation techniques are methodspermitting the site-specific modification of a plant genome. Thesemodifications can include, but are not limited to, site-specificmutations, deletions, insertions, and replacements of nucleotides. Thesemodifications can be made anywhere within the genome of a plant, forexample, in genomic elements, including, among others, coding sequences,regulatory elements, and non-coding DNA sequences. Any number of suchmodifications can be made and that number of modifications may be madein any order or combination, for example, simultaneously all together orone after another. Such methods may lead to changes in phenotype. Thetechniques for such modifications are well known in the art and include,for example, use of CRISPR-Cas systems, zinc-finger nucleases (ZFNs),and transcription activator-like effector nucleases (TALENs), amongothers.

Many hundreds if not thousands of different genes are known and couldpotentially be introduced into an alfalfa plant according to theinvention. Non-limiting examples of particular genes and correspondingphenotypes one may choose to introduce into an alfalfa plant arepresented below.

A. Male Sterility

Genetic male sterility is available in alfalfa. Although male sterilityis not required for crossing alfalfa plants, it is an efficient means bywhich to generate alfalfa varieties with increased hybridism, asgeneration of true-breeding alfalfa varieties is challenging due toalfalfa being highly self-incompatible. Alfalfa male sterility systemshave been described in, for example, U.S. Pat. Nos. 6,774,280 and7,067,721, the disclosures of which are each specifically incorporatedherein by reference in their entirety.

In one embodiment of the present invention, plants of alfalfa varietyR413A316 or plants derived therefrom may be incorporated into a breedingscheme to produce progeny with increased hybridism such as breeding withcytoplasmic male sterile lines. The present invention therefore providesa method of obtaining alfalfa populations with high hybridism usingcytoplasmic male sterile (CMS), maintainer, and pollenizer(male-fertile) alfalfa populations. The cells of the CMS alfalfa plantscontain sterile cytoplasm and a non-restorer gene. The cells of amaintainer alfalfa plants contains normal cytoplasm and the non-restorergene. The pollenizer alfalfa line is fertile, displaying both male andfemale parts.

The CMS and maintainer plants can be crossed, and the resultant seedproduced by the CMS parents would be hybrid and male sterile. Thesehybrid, male sterile seed can then be randomly bulked with pollenizerseed preferably at a ratio of 4:1, respectively. This bulked seed canthen be grown and those plants intercrossed. The resulting seed fromsuch a cross should have at least 75% hybridity, i.e., at least 75% ofthe seeds are genetically distinct from both their male and femaleparents.

Male sterile populations may be identified by evaluating pollenproduction using the Pollen Production Index (P.P.I.), which recognizesthe four distinct classes shown in Table 17.

TABLE 17 Pollen Product Index (P.P.I.) Classes. Class P.P.I.Characteristics Male Sterile 0 Visible pollen can be observed with thenaked eye Plant (MS) when flower is tripped with a black knife blade.Partial Male 0.1 A trace of pollen is found with the naked eye Sterilewhen flower is tripped with a black knife blade. Plant (PMS) PartialFertile 0.6 Less than a normal amount of pollen can be Plant (PF)observed with the naked eye when flower is tripped with a black knifeblade. Fertile 1.0 Normal amounts of pollen can be observed when Plant(F) flower is tripped with a black knife blade.

B. Herbicide Resistance

Numerous herbicide resistance genes are known and may be employed withthe invention. A non-limiting example is a gene conferring resistance toa herbicide that inhibits the growing point or meristem such asimidazolinone or sulfonylurea herbicides. As imidazolinone andsulfonylurea herbicides are acetolactate synthase (ALS)-inhibitingherbicides that prevent the formation of branched chain amino acids,exemplary genes in this category code for ALS and AHAS enzymes asdescribed, for example, by Lee et al., EMBO J., 7:1241, 1988; Gleen etal., Plant Molec. Biology, 18:1185, 1992; and Miki et al., Theor. Appl.Genet., 80:449, 1990. As a non-limiting example, a gene may be employedto confer resistance to the exemplary sulfonylurea herbicidenicosulfuron.

Resistance genes for glyphosate (resistance conferred by mutant5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyltransferase (PAT) and Streptomyces hygroscopicusphosphinothricin acetyltransferase (bar) genes) may also be used. See,for example, U.S. Pat. No. 4,940,835 to Shah et al., which discloses thenucleotide sequence of a form of EPSPS that can confer glyphosateresistance. Non-limiting examples of EPSPS transformation eventsconferring glyphosate resistance are provided by U.S. Pat. Nos.7,566,817; 8,124,848; and 9,068,196. The J-101 event disclosed in U.S.Pat. No. 7,566,817 is beneficial in conferring glyphosate tolerance inalfalfa.

A DNA molecule encoding a mutant aroA gene can be obtained under ATCCAccession No. 39256, and the nucleotide sequence of the mutant gene isdisclosed in U.S. Pat. No. 4,769,061 to Comai. A hygromycin Bphosphotransferase gene from E. coli that confers resistance toglyphosate in tobacco callus and plants is described in Penaloza-Vazquezet al., Plant Cell Reports, 14:482, 1995. European Patent ApplicationPublication No. EP0333033 to Kumada et al., and U.S. Pat. No. 4,975,374to Goodman et al., disclose nucleotide sequences of glutamine synthetasegenes that confer resistance to herbicides such as L-phosphinothricin.The nucleotide sequence of a phosphinothricin acetyltransferase gene isprovided in European Patent Application Publication No. EP0242246 toLeemans et al. DeGreef et al. (Biotechnology, 7:61, 1989) describe theproduction of transgenic plants that express chimeric bar genes codingfor phosphinothricin acetyl transferase activity. Exemplary genesconferring resistance to a phenoxy class herbicide haloxyfop and acyclohexanedione class herbicide sethoxydim are the Acct-S1, Acct-S2 andAcct-S3 genes described by Marshall et al., (Theor. Appl. Genet.,83:435, 1992). As a non-limiting example, a gene may confer resistanceto other exemplary phenoxy class herbicides that include, but are notlimited to, quizalofop-p-ethyl and 2,4-dichlorophenoxyacetic acid(2,4-D).

Genes are also known that confer resistance to herbicides that inhibitphotosynthesis such as, for example, triazine herbicides (psbA and gs+genes) and benzonitrile herbicides (nitrilase gene). As a non-limitingexample, a gene may confer resistance to the exemplary benzonitrileherbicide bromoxynil. Przibila et al. (Plant Cell, 3:169, 1991) describethe transformation of Chlamydomonas with plasmids encoding mutant psbAgenes. Nucleotide sequences for nitrilase genes are disclosed in U.S.Pat. No. 4,810,648 to Stalker, and DNA molecules containing these genesare available under ATCC Accession Nos. 53435, 67441, and 67442. Cloningand expression of DNA coding for a glutathione S-transferase isdescribed by Hayes et al. (Biochem. J., 285:173, 1992).4-hydroxyphenylpyruvate dioxygenase (HPPD) is a target of theHPPD-inhibiting herbicides, which deplete plant plastoquinone andvitamin E pools. Rippert et al. (Plant Physiol., 134:92, 2004) describesan HPPD-inhibitor resistant tobacco plant that was transformed with ayeast-derived prephenate dehydrogenase (PDH) gene. Protoporphyrinogenoxidase (PPO) is the target of the PPO-inhibitor class of herbicides; aPPO-inhibitor resistant PPO gene was recently identified in Amaranthustuberculatus (Patzoldt et al., PNAS, 103(33):12329, 2006). The herbicidemethyl viologen inhibits CO₂ assimilation. Foyer et al. (Plant Physiol.,109:1047, 1995) describe a plant overexpressing glutathione reductase(GR) that is resistant to methyl viologen treatment.

Siminszky (Phytochemistry Reviews, 5:445, 2006) describes plantcytochrome P450-mediated detoxification of multiple, chemicallyunrelated classes of herbicides. Modified bacterial genes have beensuccessfully demonstrated to confer resistance to atrazine, a herbicidethat binds to the plastoquinone-binding membrane protein QB inphotosystem II to inhibit electron transport. See, for example, studiesby Cheung et al. (PNAS, 85:391, 1988), describing tobacco plantsexpressing the chloroplast psbA gene from an atrazine-resistant biotypeof Amaranthus hybridus fused to the regulatory sequences of a nucleargene, and Wang et al. (Plant Biotech. J., 3:475, 2005), describingtransgenic alfalfa, Arabidopsis, and tobacco plants expressing the atzAgene from Pseudomonas sp. that were able to detoxify atrazine.

Bayley et al. (Theor. Appl. Genet., 83:645, 1992) describe the creationof 2,4-D-resistant transgenic tobacco and cotton plants using the 2,4-Dmonooxygenase gene tfdA from Alcaligenes eutrophus plasmid pJP5. U.S.Patent Application Publication No. 20030135879 describes the isolationof a gene for dicamba monooxygenase (DMO) from Psueodmonas maltophiliathat is involved in the conversion of dicamba to a non-toxic3,6-dichlorosalicylic acid and thus may be used for producing plantstolerant to this herbicide.

Other examples of herbicide resistance have been described, forinstance, in U.S. Pat. Nos. 6,803,501; 6,448,476; 6,248,876; 6,225,114;6,107,549; 5,866,775; 5,804,425; 5,633,435; 5,463,175.

C. Disease and Pest Resistance

Plant defenses are often activated by specific interaction between theproduct of a disease resistance gene (R) in the plant and the product ofa corresponding avirulence (Avr) gene in the pathogen. A plant line canbe transformed with a cloned resistance gene to engineer plants that areresistant to specific pathogen strains. See, for example Jones et al.(Science, 266:789-793, 1994) (cloning of the tomato Cf-9 gene forresistance to Cladosporium flavum); Martin et al. (Science,262:1432-1436, 1993) (tomato Pto gene for resistance to Pseudomonassyringae pv. tomato); and Mindrinos et al. (Cell, 78(6):1089-1099, 1994)(Arabidopsis RPS2 gene for resistance to Pseudomonas syringae).

A viral-invasive protein or a complex toxin derived therefrom may alsobe used for viral disease resistance. For example, the accumulation ofviral coat proteins in transformed plant cells imparts resistance toviral infection and/or disease development effected by the virus fromwhich the coat protein gene is derived and related viruses. See Beachyet al. (Ann. Rev. Phytopathol., 28:451, 1990). Coat protein-mediatedresistance has been conferred upon transformed plants against alfalfamosaic virus, cucumber mosaic virus, tobacco streak virus, potato virusX, potato virus Y, tobacco etch virus, tobacco rattle virus, and tobaccomosaic virus.

A virus-specific antibody may also be used. See, for example,Tavladoraki et al. (Nature, 366:469-472, 1993), who show that transgenicplants expressing recombinant antibody genes are protected from virusattack. Virus resistance has also been described in, for example, U.S.Pat. Nos. 6,617,496; 6,608,241; 6,015,940; 6,013,864; 5,850,023 and5,304,730. Additional means of inducing whole-plant resistance to apathogen include modulation of the systemic acquired resistance (SAR) orpathogenesis related (PR) genes, for example genes homologous to theArabidopsis thaliana NIM1/NPR1/SAI1, and/or by increasing salicylic acidproduction (Ryals et al., Plant Cell, 8:1809-1819, 1996).

Logemann et al. (Biotechnology, 10:305-308, 1992), for example, disclosetransgenic plants expressing a barley ribosome-inactivating gene thathave an increased resistance to fungal disease. Plant defensins may beused to provide resistance to fungal pathogens (Thomma et al., Planta,216:193-202, 2002). Other examples of fungal disease resistance areprovided in U.S. Pat. Nos. 6,653,280; 6,573,361; 6,506,962; 6,316,407;6,215,048; 5,516,671; 5,773,696; 6,121,436; and 6,316,407.

Nematode resistance has been described in, for example, U.S. Pat. No.6,228,992, and bacterial disease resistance has been described in, forexample, U.S. Pat. No. 5,516,671.

D. Insect Resistance

One example of an insect resistance gene includes a Bacillusthuringiensis protein, a derivative thereof, or a synthetic polypeptidemodeled thereon. See, for example, Geiser et al. (Gene, 48(1):109-118,1986), who disclose the cloning and nucleotide sequence of a Bacillusthuringiensis δ-endotoxin gene. Moreover, DNA molecules encodingδ-endotoxin genes are deposited under ATCC Accession Nos. 40098, 67136,31995, and 31998. Another example is a lectin. See, for example, VanDamme et al., (Plant Molec. Biol., 24:825-830, 1994), who disclose thenucleotide sequences of several Clivia miniata mannose-binding lectingenes. A vitamin-binding protein may also be used, such as, for example,avidin. See PCT Application No. US93/06487, the contents of which arehereby incorporated by reference. This application teaches the use ofavidin and avidin homologues as larvicides against insect pests.

Yet another insect resistance gene is an enzyme inhibitor, for example,protease, proteinase, or amylase inhibitors. See, for example, Abe etal. (J. Biol. Chem., 262:16793-16797, 1987) describing the nucleotidesequence of a rice cysteine proteinase inhibitor; Linthorst et al.(Plant Molec. Biol., 21:985-992, 1993) describing the nucleotidesequence of a cDNA encoding tobacco proteinase inhibitor I; and Sumitaniet al. (Biosci. Biotech. Biochem., 57:1243-1248, 1993) describing thenucleotide sequence of a Streptomyces nitrosporeus α-amylase inhibitor.

An insect-specific hormone or pheromone may also be used. See, forexample, the disclosure by Hammock et al. (Nature, 344:458-461, 1990) ofbaculovirus expression of cloned juvenile hormone esterase, aninactivator of juvenile hormone; Gade and Goldsworthy (Eds.Physiological System in Insects, Elsevier Academic Press, Burlington,Mass., 2007), describing allostatins and their potential use in pestcontrol; and Palli et al. (Vitam. Horm., 73:59-100, 2005), disclosinguse of ecdysteroid and ecdysteroid receptor in agriculture. The diuretichormone receptor (DHR) was identified in Price et al. (Insect Mol.Biol., 13:469-480, 2004) as another potential candidate target ofinsecticides.

Still other examples include an insect-specific antibody or animmunotoxin derived therefrom and a developmental-arrestive protein. SeeTaylor et al. (Seventh Int'l Symposium on Molecular Plant-MicrobeInteractions, Edinburgh, Scotland, Abstract W97, 1994), who describedenzymatic inactivation in transgenic tobacco via production ofsingle-chain antibody fragments. Numerous other examples of insectresistance have been described. See, for example, U.S. Pat. Nos.6,809,078; 6,713,063; 6,686,452; 6,657,046; 6,645,497; 6,642,030;6,639,054; 6,620,988; 6,593,293; 6,555,655; 6,538,109; 6,537,756;6,521,442; 6,501,009; 6,468,523; 6,326,351; 6,313,378; 6,284,949;6,281,016; 6,248,536; 6,242,241; 6,221,649; 6,177,615; 6,156,573;6,153,814; 6,110,464; 6,093,695; 6,063,756; 6,063,597; 6,023,013;5,959,091; 5,942,664; 5,942,658, 5,880,275; 5,763,245; and 5,763,241.

E. Modified Fatty Acid, Phytate, and Carbohydrate Metabolism

Genes may be used conferring modified fatty acid metabolism. Forexample, stearyl-ACP desaturase genes may be used, see Knutzon et al.(Proc. Natl. Acad. Sci. USA, 89:2624-2628, 1992). Various fatty aciddesaturases have also been described. McDonough et al. describe aSaccharomyces cerevisiae OLE1 gene encoding Δ9-fatty acid desaturase, anenzyme which forms the monounsaturated palmitoleic (16:1) and oleic(18:1) fatty acids from palmitoyl (16:0) or stearoyl (18:0) CoA (J.Biol. Chem., 267(9):5931-5936, 1992). Fox et al. describe a geneencoding a stearoyl-acyl carrier protein Δ9-desaturase from castor(Proc. Natl. Acad. Sci. USA, 90(6):2486-2490, 1993). Reddy et al.describe Δ6- and Δ12-desaturases from the cyanobacteria Synechocystisresponsible for the conversion of linoleic acid (18:2) togamma-linolenic acid (18:3 gamma) (Plant Mol. Biol., 22(2):293-300,1993). Arondel et al. describe a gene from Arabidopsis thaliana thatencodes an omega-3 desaturase (Science, 258(5086):1353-1355, 1992).Plant Δ9-desaturases as well as soybean and Brassica Δ15-desaturaseshave also been described, see PCT Application Publication No. WO91/13972 and European Patent Application Publication No. EP0616644,respectively. U.S. Pat. No. 7,622,632 describes fungal Δ15-desaturasesand their use in plants. European Patent Application Publication No.EP1656449 describes Δ6-desaturases from Primula.

Modified oil production is disclosed in, for example, U.S. Pat. Nos.6,444,876; 6,426,447; and 6,380,462. High oil production is disclosedin, for example, U.S. Pat. Nos. 6,495,739; 5,608,149; 6,483,008; and6,476,295. Modified fatty acid content is disclosed in, for example,U.S. Pat. Nos. 6,828,475; 6,822,141; 6,770,465; 6,706,950; 6,660,849;6,596,538; 6,589,767; 6,537,750; 6,489,461 and 6,459,018.

Phytate metabolism may also be modified by introduction of aphytase-encoding gene to enhance breakdown of phytate, adding more freephosphate to the transformed plant. For example, see Van Hartingsveldtet al. (Gene, 127:87-94, 1993), for a disclosure of the nucleotidesequence of an Aspergillus niger phytase gene, and see Raboy et al.(Plant Physiol., 124(1):355-368, 2000) for the disclosure of low phyticacid mutant maize alleles lpa1-1 and lpa2-1.

A number of genes are known that may be used to alter carbohydratemetabolism. For example, plants may be transformed with a gene codingfor an enzyme that alters the branching pattern of starch. For example,Shiroza et al. (J. Bacteriol., 170:810-816, 1988) describe a nucleotidesequence of the Streptococcus mutans fructosyltransferase gene;Steinmetz et al. (Mol. Gen. Genet., 20:220-228, 1985) describe anucleotide sequence of the Bacillus subtilis levansucrase gene; Pen etal. (Biotechnology, 10:292-296, 1992) describe production of transgenicplants that express Bacillus licheniformis α-amylase; Elliot et al.(Plant Molec. Biol., 21:515-524, 1993) describe nucleotide sequences oftomato invertase genes; Sergaard et al. (J. Biol. Chem., 268:22480,1993) describe site-directed mutagenesis of a barley α-amylase gene; andFisher et al. (Plant Physiol., 102:1045-1046, 1993) describe maizeendosperm starch branching enzyme II. The Z10 gene encoding a 10 kD zeinstorage protein from maize may also be used to alter the quantities of10 kD zein in the cells relative to other components (Kirihara et al.,Gene, 71(2):359-370, 1988).

F. Resistance to Abiotic Stress

Abiotic stress includes dehydration or other osmotic stress, salinity,high or low light intensity, high or low temperatures, submergence,exposure to heavy metals, and oxidative stress.Delta-pyrroline-5-carboxylate synthetase (P5CS) from mothbean has beenused to provide protection against general osmotic stress.Mannitol-1-phosphate dehydrogenase (mt1D) from E. coli has been used toprovide protection against drought and salinity. Choline oxidase (codAfrom Arthrobactor globiformis) can protect against cold and salt. E.coli choline dehydrogenase (betA) provides protection against salt.Additional protection from cold can be provided by omega-3-fatty aciddesaturase (fad7) from Arabidopsis thaliana. Trehalose-6-phosphatesynthase and levan sucrase (SacB) from yeast and Bacillus subtilis,respectively, can provide protection against drought (summarized fromAnnex II Genetic Engineering for Abiotic Stress Tolerance in Plants,Consultative Group On International Agricultural Research TechnicalAdvisory Committee). Overexpression of superoxide dismutase can be usedto protect against superoxides, see U.S. Pat. No. 5,538,878.

G. Additional traits

Additional traits can be introduced into alfalfa variety R413A316. Anon-limiting example of such a trait is a coding sequence whichdecreases RNA and/or protein levels. The decreased RNA and/or proteinlevels may be achieved through RNAi methods, such as those described inU.S. Pat. No. 6,506,559.

Another trait that may find use with alfalfa variety R413A316 is asequence which allows for site-specific recombination. Examples of suchsequences include the FRT sequence used with the FLP recombinase (Zhuand Sadowski, J. Biol. Chem., 270:23044-23054, 1995) and the LOXsequence used with CRE recombinase (Sauer, Mol. Cell. Biol.,7:2087-2096, 1987). The recombinase genes can be encoded at any locationwithin the genome of the alfalfa plant and are active in the hemizygousstate.

In certain embodiments alfalfa plants may be made more tolerant to ormore easily transformed with Agrobacterium tumefaciens. For example,expression of p53 and iap, two baculovirus cell-death suppressor genes,inhibited tissue necrosis and DNA cleavage. Additional targets mayinclude plant-encoded proteins that interact with the Agrobacterium Virgenes; enzymes involved in plant cell wall formation; and histones,histone acetyltransferases and histone deacetylases (reviewed in Gelvin,Microbiology & Mol. Biol. Reviews, 67:16-37, 2003).

In addition to the modification of oil, fatty acid, or phytate contentdescribed above, certain embodiments may modify the amounts or levels ofother compounds. For example, the amount or composition of antioxidantscan be altered. See, for example, U.S. Pat. Nos. 6,787,618 and 7,154,029and International Patent Application Publication No. WO 00/68393, whichdisclose the manipulation of antioxidant levels, and InternationalPatent Application Publication No. WO 03/082899, which discloses themanipulation of an antioxidant biosynthetic pathway. In otherembodiments the level of lignin may altered. See, for example, U.S. Pat.Nos. 9,670,498; 9,701,976; and 9,854,778, which disclose event KK179-2.The KK179-2 event is beneficial in reducing lignin in alfalfa plants.The event encodes dsRNA that suppress endogenousS-adenosyl-L-methionine: trans-caffeoyl CoA 3-O-methyltransferaselevels, which consequently suppresses lignin production.

In certain embodiments alfalfa plants may be modified to augment theirnitrogen fixation capacity. In specific embodiments, this may comprise agenetic modification that augments the intrinsic physiology ormorphology of alfalfa that enables or facilitates nitrogen fixation. Inother embodiments, modifications may augment the interactions, includingbiological interactions, between an alfalfa plant and nitrogen fixingbacteria such as, for example, Sinorhizobium meliloti.

Additionally, seed amino acid content may be manipulated. U.S. Pat. No.5,850,016 and International Patent Application Publication No. WO99/40209 disclose the alteration of the amino acid compositions ofseeds. U.S. Pat. Nos. 6,080,913 and 6,127,600 disclose methods ofincreasing accumulation of essential amino acids in seeds.

U.S. Pat. No. 5,559,223 describes synthetic storage proteins of whichthe levels of essential amino acids can be manipulated. InternationalPatent Application Publication No. WO 99/29882 discloses methods foraltering amino acid content of proteins. International PatentApplication Publication No. WO 98/20133 describes proteins with enhancedlevels of essential amino acids. International Patent ApplicationPublication No. WO 98/56935 and U.S. Pat. Nos. 6,346,403; 6,441,274; and6,664,445 disclose plant amino acid biosynthetic enzymes. InternationalPatent Application Publication No. WO 98/45458 describes synthetic seedproteins having a higher percentage of essential amino acids thanwild-type.

U.S. Pat. No. 5,633,436 discloses plants comprising a higher content ofsulfur-containing amino acids; U.S. Pat. No. 5,885,801 discloses plantscomprising a high threonine content; U.S. Pat. Nos. 5,885,802 and5,912,414 disclose plants comprising a high methionine content; U.S.Pat. No. 5,990,389 discloses plants comprising a high lysine content;U.S. Pat. No. 6,459,019 discloses plants comprising an increased lysineand threonine content; International Patent Application Publication No.WO 98/42831 discloses plants comprising a high lysine content;International Patent Application Publication No. WO 96/01905 disclosesplants comprising a high threonine content; and International PatentApplication Publication No. WO 95/15392 discloses plants comprising ahigh lysine content.

Tissue Cultures and In Vitro Regeneration of Alfalfa Plants

A further aspect of the invention relates to tissue cultures of alfalfavariety R413A316. As used herein, the term “tissue culture” indicates acomposition comprising isolated cells of the same or a different type ora collection of such cells organized into parts of a plant. Exemplarytypes of tissue cultures are protoplasts, calli, and plant cells thatare intact in plants or parts of plants, such as embryos, pollen,flowers, leaves, roots, root tips, anthers, and the like. In oneembodiment, the tissue culture comprises embryos, protoplasts,meristematic cells, pollen, leaves, or anthers.

Exemplary procedures for preparing tissue cultures of regenerablealfalfa cells and regenerating alfalfa plants therefrom are disclosed inU.S. Pat. No. 5,324,646, which is specifically incorporated herein byreference in its entirety. Tissue culture of alfalfa is furtherdescribed in Saunders, J. W. and Bingham, E. T., Production of alfalfaplants from callus tissue, Crop Sci 12:804-808 (1971), and incorporatedherein by reference.

An important ability of a tissue culture is the capability to regeneratefertile plants. This allows, for example, transformation of the tissueculture cells followed by regeneration of transgenic plants. Fortransformation to be efficient and successful, DNA must be introducedinto cells that give rise to plants or germ-line tissue.

Plants typically are regenerated via two distinct processes: shootmorphogenesis and somatic embryogenesis. Shoot morphogenesis is theprocess of shoot meristem organization and development. Shoots grow outfrom a source tissue and are excised and rooted to obtain an intactplant. During somatic embryogenesis, an embryo (similar to the zygoticembryo), containing both shoot and root axes, is formed from somaticplant tissue. An intact plant rather than a rooted shoot results fromthe germination of the somatic embryo.

Shoot morphogenesis and somatic embryogenesis are different processesand the specific route of regeneration is primarily dependent on theexplant source and media used for tissue culture manipulations. Whilethe systems are different, both systems show variety-specific responsesin which some lines are more responsive to tissue culture manipulationsthan others. A line that is highly responsive in shoot morphogenesis maynot generate many somatic embryos. Lines that produce large numbers ofembryos during an ‘induction’ step may not give rise to rapidly-growingproliferative cultures. Therefore, it may be desired to optimize tissueculture conditions for each alfalfa line. These optimizations mayreadily be carried out by one of skill in the art of tissue culturethrough small-scale culture studies. In addition to line-specificresponses, proliferative cultures can be observed with both shootmorphogenesis and somatic embryogenesis. Proliferation is beneficial forboth systems as it allows a single, transformed cell to multiply to thepoint that it will contribute to germ-line tissue.

Embryogenic cultures can also be used successfully for regeneration,including regeneration of transgenic plants, if the origin of theembryos is recognized and the biological limitations of proliferativeembryogenic cultures are understood. Biological limitations include thedifficulty in developing proliferative embryogenic cultures and reducedfertility problems (culture-induced variation) associated with plantsregenerated from long-term proliferative embryogenic cultures. Some ofthese problems are accentuated in prolonged cultures. The use of morerecently cultured cells may decrease or eliminate such problems.

Definitions

In the description and tables, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, the following definitions are provided:

A: When used in conjunction with the word “comprising” or other openlanguage in the claims, the words “a” and “an” denote “one or more.”

About: Refers to embodiments or values that include the standarddeviation of the mean for a given item being measured.

Acid-Detergent Fiber (ADF): A measurement that approximates the amountof cellulose fiber and ash present in a feed. Forages with high ADFvalues are less digestible than forages with low ADF values, andtherefore provide fewer nutrients to the animal through digestion.Because of this relationship, ADF serves as an estimate of digestibilityand can be used by nutritionists to predict the energy that will beavailable from a forage.

Allele: Any of one or more alternative forms of a locus. In a diploidcell or organism, the two alleles of a given locus occupy correspondingloci on a pair of homologous chromosomes.

AOSCA: The abbreviation for the Association of Official Seed CertifyingAgencies.

Backcrossing: A process in which a breeder repeatedly crosses hybridprogeny, for example a first generation hybrid (F₁), back to one of theparents of the hybrid progeny. Backcrossing can be used to introduce oneor more single locus conversions from one genetic background intoanother.

Check Cultivars: A single set of check cultivars that represent falldormancy classes (FDC) 1 to 11. These check cultivars have been selectedto maintain the intended relationship between the original set of ninecheck cultivars (Standard Tests, March 1991, updated in 1998) and tohave minimal variation across environments. The actual fall dormancyrating (FDR) is based on the average University of Californiaregression. The Certified Alfalfa Seed Council Class that each checkcultivar represents is listed below in Table 18.

Crossing: The mating of two plants.

Cross-pollination: Fertilization by the union of two gametes fromdifferent plants.

Crude Protein (CP): A measurement in which the total nitrogenconcentration of a forage is multiplied by 6.25. This technique measuresnot only the nitrogen present in true proteins, but also that present innon-protein forms such as ammonia, urea and nitrate. Because most of thenon-protein forms of nitrogen are converted to true protein by the rumenmicroorganisms, CP is considered by nutritionists to provide an accuratemeasure of the protein that will be available to ruminant animals from agiven forage.

Dietary Dry Matter (DM): The matter e.g., protein, fiber, fat, minerals,etc., within a sample of alfalfa excluding water. It is one metric bywhich yield may be calculated.

Emasculate: The removal of plant male sex organs or the deactivation ofthe organs with a cytoplasmic or nuclear genetic factor or a chemicalagent conferring male sterility.

Enzymes: Molecules which can act as catalysts in biological reactions.

F₁ Hybrid: The first filial generation of progeny derived from a crossbetween two plants of different genotypes.

Fall Dormancy (Dormancy or FD): Most alfalfa plants go dormant in thefall in preparation for winter. This is characterized by a reduction ingrowth rates and metabolism as well as the storage of carbohydrate inthe root system of the plants. The onset of dormancy is genotypedependent and is triggered by a combination of day length andtemperature. The dormancy response of alfalfa genotypes can bequantified by measuring plant height in autumn relative to a set ofstandard check varieties.

Fall dormancy test: The test requires that plants are cut off in earlySeptember with plant height measured in early-mid October. Early falldormant types show very little regrowth after the September clipping;whereas, later fall dormant types demonstrate substantial growth. Thefall dormancy groups are numbered 1 to 11, in which Dormancy Group 1 ismost dormant and suited for cold climates, i.e., these varieties wouldstop growing and go dormant over winter, and Dormancy Groups 7-11 arevery non-dormant and would continue to regrow after fall cuttings.Dormancy groups 7-11 are suited for warm to very hot climates, and wouldhave relatively high winter activity. The NA&MLVRB recognizes standardor check varieties for Dormancy Groups 1-11. The check varieties for thevarious fall dormancy ratings/Dormancy Groups (corresponding to therating scale used by the Certified Alfalfa Seed Council (CASC)) arelisted in Table 18.

Genetic Dosage: The number of copies of a particular gene, allele,locus, or transgene that are present in the genome of an organism.Alfalfa as an autotetraploid may contain genes, alleles, loci, ortransgenes in at least simplex, duplex, triplex, or quadraplex dosages.

Genetic Complement: An aggregate of nucleotide sequences, the expressionof which sequences defines the phenotype in alfalfa plants, orcomponents of plants including cells or tissue.

Genotype: The genetic constitution of a cell or organism.

Haploid: A cell or organism having one set of the two sets ofchromosomes in a diploid.

Haplotype Analysis: A genetic profile of a particular organism in whichgenetic markers, typically SNPs, and linkage maps are used to identifythe parent and/or earlier ancestors from which one or more genetic lociwere inherited.

Isozymes: Detectable variants of an enzyme, the variants catalyzing thesame reaction(s) but differing from each other, e.g., in primarystructure and/or electrophoretic mobility. The differences betweenisozymes are under single gene, codominant control. Consequently,electrophoretic separation to produce band patterns can be equated todifferent alleles at the DNA level. Structural differences that do notalter charge cannot be detected by this method.

In Vitro True Digestibility (IVTD): A measurement of digestibilityutilizing actual rumen microorganisms. Although ADF serves as a goodestimate of digestibility, IVID provides a more accurate assessment of aforage's feeding value by actually measuring the portion of a foragethat is digested. This process is more expensive and time consuming thanthe analysis for ADF concentrations of a feed, but provides a moremeaningful measure of forage digestibility. Techniques for measuring invitro digestibility are based on incubating a forage sample in asolution containing rumen microorganisms for an extended period of time(usually 48 hours).

Linkage: A phenomenon wherein alleles on the same chromosome tend tosegregate together more often than expected by chance if theirtransmission was independent. Marker: A readily detectable phenotype,preferably inherited in co-dominant fashion (both alleles at a locus ina diploid heterozygote are readily detectable), with no environmentalvariance component, i.e., heritability of 1.

Milk Per Acre: A measurement that combines “milk per ton” and “drymatter yield per acre” that is widely used as an estimate of theeconomic value of a forage.

Milk Per Ton: A measurement that characterizes forage quality in whichthe ratio of milk produced to forage consumed is estimated. The initialequation that was used to calculate “milk per ton” relied primarily onADF and NDF as estimates of the energy content and potential intake ofthe forage, respectively. After subtracting the amount of energyrequired for daily maintenance of the cow, the quantity of milk thatcould be produced from the remaining energy is calculated. The ratio ofmilk produced to forage consumed is then reported in the units of poundsof milk produced per ton of forage consumed. The standard equation for“milk per ton” has since been modified multiple times to increaseaccuracy and each of these modified equations are well known in the art.For instance, the MILK2006 formula uses forage analyses, e.g., crudeprotein, NDF, in vitro NDF digestibility, and non-fiber carbohydrate(NFC), to estimate both forage energy content and DM intake from NDF.

NAAIC: The abbreviation for the North America Alfalfa ImprovementConference, which is the governing body of the NA&MLVRB.

NA&MLVRB: The abbreviation for the National Alfalfa and MiscellaneousLegume Variety Review Board. The NA&MLVRB is administered by theAssociation of Official Seed Certifying Agencies (AOSCA) and waspreviously known as the National Alfalfa Variety Review Board (NAVRB).

Neutral-Detergent Fiber (NDF): A measurement that represents the totalamount of fiber present in the alfalfa. Because fiber is the portion ofthe plant most slowly digested in the rumen, it is this fraction thatfills the rumen and becomes a limit to the amount of feed an animal canconsume. The higher the NDF concentration of a forage, the slower therumen will empty reducing what an animal will be able to consume. Forthis reason, NDF is used by nutritionists as an estimate of the quantityof forage that an animal will be able to consume. Forages with high NDFlevels can limit intake to the point that an animal is unable to consumeenough feed to meet their energy and protein requirements.

Or: As used herein is meant to mean “and/or” and be interchangeabletherewith unless explicitly indicated to refer to the alternative only.

Persistence: The quality of the alfalfa stand in terms of both planthealth and the number of plants over seasons. Persistence of an alfalfavariety is measured, typically in its area of adaptation, by visuallyestimating percent ground cover both in the establishment year(“Initial”) and at least 24 months later (“Final”).

Phenotype: The detectable characteristics of a cell or organism, whichare the manifestation of gene expression.

Phenotypic Score (PSC): The phenotypic score is a visual rating of thegeneral appearance of the variety. All visual traits are considered inthe score, including healthiness, standability, appearance, and freedomfrom disease. Ratings are scored as 1 being poor to 9 being excellent.

Potato Leafhopper Resistance: A reaction of the alfalfa host plant whichenables it to avoid serious damage from potato leafhopper feeding. Aresistant plant demonstrates normal growth despite the feeding of potatoleafhoppers. Susceptible plants show significant stunting and yellowingas a result of potato leafhopper feeding. Potato leafhopper resistanceof alfalfa cultivars is characterized as a combination of percentresistance and average severity index (ASI). The National AlfalfaVariety Review Board has adopted a rating system based on percent ofresistant plants to describe levels of pest. The ratings are susceptible(0-5%); low resistance (6-15%); moderate resistance (16-30%); resistance(31-50%); and high resistance (>51%). The average severity index (ASI)of a variety is the average damage score for 100 random plants.Individual plants are scored on a (1-5) scale, where “1” corresponds to“no damage evident” and “5” corresponds to “severe stunting andyellowing.” Plants scored as “1” and “2” are classified as resistant.

Quantitative Trait Loci (QTL): Genetic loci that contribute, at least inpart, certain numerically representable traits that are usuallycontinuously distributed.

Regeneration: The development of a plant from tissue culture.

Relative Feed Value (RFV) is a numeric value assigned to forages basedupon their ADF and NDF values. In this calculation, NDF is used toestimate the dry matter intake expected for a given forage, and the ADFconcentration is used to estimate the digestibility of the forage. Bycombining these two relationships, an estimate of digestible dry matterintake is generated. This value is then reported relative to a standardforage (fall bloom alfalfa=100), and can be used to rank forages basedon their anticipated feeding value. Relative feed value has beenaccepted in many areas as a means of estimating forage feeding value andis commonly used in determining the price of alfalfa at tested hayauctions.

Relative Forage Quality (RFQ): A numeric value that estimates the energycontent of forage for total digestible nutrients as recommended by theNational Research Council. Values are assigned to forages based upon thedry matter intake (DMI), which can be estimated by NDF, and TotalDigestible Nutrients (TDN). By combining these two relationships, anestimate of how the forage will perform in animal rations is predicted.Relative forage quality has been accepted in many areas as a means ofestimating forage feeding value and is commonly used in determining theprice of alfalfa at tested hay auctions or for on farm use.

Self-pollination: The transfer of pollen from the anther to the stigmaof the same plant.

Single Locus Converted (Conversion) Plant: Plants that are developed bya plant breeding technique called backcrossing and/or by genetictransformation to introduce a given locus that may be transgenic inorigin, in which essentially all of the morphological and physiologicalcharacteristics of an alfalfa variety are recovered in addition to thecharacteristics of the locus transferred into the alfalfa variety viathe backcrossing technique or by genetic transformation. It isunderstood that once introduced into any alfalfa plant genome, a locusthat is transgenic in origin (transgene), can be introduced bybackcrossing as with any other locus. A single locus may comprise onegene, or in the case of transgenic plants, one or more transgenesintegrated into the host genome at a single site (locus).

SNP profile: A profile in which single nucleotide polymorphisms (SNPs)are used as genetic markers. SNP detection methods that may be used togenerate such a profile are well-known in the art and include, but arenot limited to, dynamic allele-specific hybridization, molecularbeacons, microarrays, restriction enzyme digestions, tetra-primeramplification refractory mutation system PCR, primer extension, TaqMan,and next-generation sequencing.

SSR profile: A profile of simple sequence repeats used as geneticmarkers and scored by gel electrophoresis following PCR amplificationusing flanking oligonucleotide primers.

Substantially Equivalent: A characteristic that, when compared, does notshow a statistically significant difference from the mean, e.g., p=0.05.

Synthetic variety 1 (SYN1): A variety that is developed by intercrossinga number of genotypes with specific favorable characteristics and/oroverall general favorable qualities. Synthetic (SYN) varieties can bedeveloped by using clones, inbreds, open-pollinated varieties, and/orindividual heterozygous plants.

Synthetic variety 1+n (SYN(1+n)): A variety that descends from a Syn1and is produced by randomly intercrossing plants of the previousgeneration so that allele frequencies are maintained from one generationto the next. For example, a Syn2 is produced by randomly crossing Syn1plants, and randomly crossing those Syn2 plants produces a Syn3.

Tons per Acre (TA): A measurement of the tons of alfalfa produced peracre of land, which is used to calculate yield. Typically thismeasurement is made using harvested alfalfa that has been dried, whichmay be denoted as “DM in T/A” or “Tons DM/Acre.”

Tissue Culture: A composition comprising isolated cells of the same or adifferent type or a collection of such cells organized into parts of aplant.

Total Digestible Nutrients (TDN): An estimate of the energy content of afeedstuff based on its relative proportions of fiber, fat, carbohydrate,crude protein, and ash. Because it is expensive to measure each of thesecomponents, TDN is usually estimated from ADF or IVTD. Although stillused in some areas as a criteria for evaluating alfalfa hay at auctions,TDN has been shown to overestimate the energy content of low qualityforages and thus does not accurately reflect the nutritional value ofall forage samples.

Transgene: A genetic sequence that has been introduced into the genomeof a alfalfa plant by transformation or site-specific recombination.

Winterhardiness (WH): An estimate of the ability of an alfalfa plant tosurvive the stresses associated with winter. Cold hardiness is a keyfeature of the winterhardiness trait. There is a general relationshipbetween fall dormancy and winterhardiness, the early fall dormant types(FD2-5) are more winterhardy than the later fall dormant types (FD6-9).The winterhardiness rating used in this patent are derived from thestandard test for measuring winter survival. The standard test measuresplant survival and spring vigor following a winter stress enough tosubstantially injure check varieties.

TABLE 18 Check Cultivar Fall Dormancy Ratings (FDR) and Fall DormancyClasses (FDC). VARIETY FDR¹ FDC² Maverick 0.8 1.0 Vernal 2.0 2.0 52463.4 3.0 Legend 3.8 4.0 Archer 5.3 5.0 ABI 700 6.3 6.0 Doria Ana 6.7 7.0Pierce 7.8 8.0 CUF 101 8.9 9.0 UC 1887 9.9 10.0 UC 1465 11.2 11.0 ¹TheFDR number corresponds to the value calculated using the University ofCalifornia regression equation. ²The FDC number corresponds to falldormancy class used by the Certified Alfalfa Seed Council (CASC).

DEPOSIT INFORMATION

A deposit of alfalfa variety R413A316, which is disclosed herein aboveand referenced in the claims, was made with the American Type CultureCollection (ATCC), 10801 University Blvd., Manassas, Va. 20110-2209. Thedate of deposit is ______ and the accession number for those depositedseeds of alfalfa variety R413A316 is ATCC Accession No. PTA-______. Allrestrictions upon the deposit have been removed, and the deposit isintended to meet all of the requirements of the Budapest Treaty and 37C.F.R. § 1.801-1.809. The deposit will be maintained in the depositoryfor a period of 30 years, or 5 years after the last request, or for theeffective life of the patent, whichever is longer, and will be replacedif necessary during that period.

All of the compositions and methods disclosed and claimed herein can bemade and executed without undue experimentation in light of the presentdisclosure. While the compositions and methods of this invention havebeen described in terms of the foregoing illustrative embodiments, itwill be apparent to those of skill in the art that variations, changes,modifications, and alterations may be applied to the composition,methods, and in the steps or in the sequence of steps of the methodsdescribed herein, without departing from the true concept, spirit, andscope of the invention. More specifically, it will be apparent thatcertain agents that are both chemically and physiologically related maybe substituted for the agents described herein while the same or similarresults would be achieved. All such similar substitutes andmodifications apparent to those skilled in the art are deemed to bewithin the spirit, scope, and concept of the invention as defined by theappended claims.

The references cited herein, to the extent that they provide exemplaryprocedural or other details supplementary to those set forth herein, arespecifically incorporated herein by reference.

1. A seed of alfalfa variety R413A316, wherein representative seed ofsaid alfalfa variety have been deposited under NCMA Accession No.202002019.
 2. A plant grown from the seed of claim 1 or a plant partthereof, wherein the plant part comprises at least one cell of saidalfalfa variety R413A316.
 3. A tissue culture of regenerable cells orregenerable protoplasts from the plant or plant part of claim
 2. 4. Thetissue culture according to claim 3, comprising cells or protoplastsfrom a plant part selected from the group consisting of leaves, roots,root tips, root hairs, anthers, pistils, stamens, pollen, ovules,flowers, seeds, embryos, stems, buds, cotyledons, hypocotyls, cells, andprotoplasts.
 5. An alfalfa plant regenerated from the tissue culture ofclaim 3, wherein the regenerated plant has all of the physiological andmorphological characteristics of a plant of said alfalfa varietyR413A316.
 6. A composition comprising the seed of claim 1 that iscomprised in plant seed growth media.
 7. The composition of claim 6,wherein the plant seed growth media is soil or a synthetic cultivationmedia.
 8. A method for producing a first generation progeny alfalfaseed, the method comprising crossing the plant of claim 2 with itself ora second alfalfa plant and harvesting the resultant alfalfa seed.
 9. Themethod of claim 8, wherein the second alfalfa plant is a plant ofalfalfa variety R413A316; wherein representative seed of said alfalfavariety have been deposited under NCMA Accession No.
 202002019. 10. Afirst generation progeny alfalfa seed produced by the method of claim 8;wherein the first generation progeny alfalfa seed has all of thephysiological and morphological characteristics of a seed of saidalfalfa variety R413A316.
 11. An alfalfa plant produced by growing theseed of claim 10; wherein the plant produced has all of thephysiological and morphological characteristics of a plant of saidalfalfa variety R413A316.
 12. A method of vegetatively propagating theplant of claim 2, the method comprising the steps of: (a) collecting atissue capable of being propagated from the plant; (b) cultivating thetissue to obtain proliferated shoots; and (c) rooting the proliferatedshoots to obtain rooted plantlets.
 13. The method of claim 12, furthercomprising growing a plant from the rooted plantlets.
 14. A method ofmodifying an alfalfa plant, wherein the method comprises introducing atransgene or a single locus conversion into the plant of claim
 2. 15.The alfalfa plant produced by the method of claim 14; wherein thealfalfa plant produced otherwise comprises all of the physiological andmorphological characteristics of a plant of said alfalfa varietyR413A316.
 16. The plant of claim 15, wherein the transgene or singlelocus comprises a nucleic acid sequence that enables site-specificgenetic recombination or confers a trait selected from the groupconsisting of male sterility, herbicide tolerance, insect resistance,pest resistance, disease resistance, improved digestibility, improvedenergy content, improved forage or seed yield, improved winterhardiness,improved nitrogen fixation, modified fatty acid metabolism, abioticstress resistance, flowering time, altered seed amino acid composition,and modified carbohydrate metabolism.
 17. A seed that produces the plantof claim 15; wherein the seed otherwise comprises all of thephysiological and morphological characteristics of a seed of saidalfalfa variety R413A316.
 18. A method of introducing a single-locusconversion into the plant of claim 2, the method comprising: (a)crossing said plant with a second alfalfa plant to produce a firstgeneration of progeny plants, wherein the second alfalfa plant comprisesthe single locus; and (b) selecting a progeny plant that comprises thesingle locus.
 19. The method of claim 18, wherein the single locuscomprises a transgene.
 20. An alfalfa plant produced by the method ofclaim 18; wherein the alfalfa plant produced otherwise comprises all ofthe physiological and morphological characteristics of a plant of saidalfalfa variety R413A316.
 21. A seed that produces the plant of claim20; wherein the seed otherwise comprises all of the physiological andmorphological characteristics of a seed of said alfalfa varietyR413A316.
 22. A method for introducing a transgene or a single locusconversion into a population of alfalfa plants, the method comprisingthe steps of: (a) modifying the plant of claim 2 by introducing atransgene or a single locus conversion; and (b) crossing the modifiedalfalfa plant of step (a) with a population of alfalfa plants to producea population of progeny plants, wherein at least a progeny plantcomprises the transgene or single locus conversion.
 23. The method ofclaim 22, further comprising the step of: (c) applying a selectiontechnique to the population produced in step (b) to select said progenyplants that comprise the transgene or single locus conversion.
 24. Amethod of producing a synthetic alfalfa variety, the method comprisingcombining the seed of claim 1 with seed of a second alfalfa variety. 25.A method of producing a commodity plant product, the method comprisingproducing the commodity plant product from the plant of claim
 2. 26. Themethod of claim 25, wherein the commodity plant product is selected froma group consisting of sprouts, forage, hay, greenchop, and silage.
 27. Acommodity plant product produced by the method of claim 25, wherein thecommodity plant product comprises at least one cell of said alfalfavariety R413A316.